[HTC One A9] jmanley69:
I had rooted my phone months ago with the original method (thanks jcase), and I thought I'd share my experience applying the new OTA from Sprint.

First off all, let me say that I have s-off, so what you read here may not work for you without that, but sunshine can s-off very easily and quickly http://theroot.ninja/

As you know, you cannot apply an OTA with a custom recovery. So the "normal" way to do this would be to throw the stock recovery (if you backed it up or extract it from the OTA) back on the phone and let the update apply. Of course, if you've mounted system r/w then you'd need to reflash your nandroid backup of your system partition before the update will work. The big problem I see in doing this is that the update will also flash the boot partition, and I'm assuming that upon first boot your internal storage will get encrypted (because you are running stock boot). That's not necessarily a bad thing unless you want to keep root, then you'd have to wipe your data partition and start loading your phone all over again - BIG pain!

So I came up with this method and it worked great for me.

**** BACKUP YOUR PHONE ****

I did a nandroid backup from TWRP before I started, but I never needed to restore from it. However, if you lose something and don't have a backup, don't blame me.

I may have rebooted more than I needed to, but it only takes a few seconds and it doesn't hurt.

Step 1 - get the system.img and firmware.zip for the latest version. You can download the RUU from HTC and then use the HTC RUU/ROM Decryption Tool and extract these from the RUU, or you can download what I already extracted (this is 1.8gb so be patient downloading)

Now, you should have system.img and firmware.zip. I'm not going to go into detail on how to install and use adb and fastboot (if you're here and have a rooted & s-off phone, then you should know this already).

Go ahead and get your recovery ready. I used the latest TWRP twrp-2.8.8.1-hiae.img

Also, while you're at it, get your SuperSU. I grabbed the latest beta 2.67 and it seems to be working, but if you're not that daring then get the latest stable version

I'm going to just list the commands and not explain them too much... Again, if you've made it this far then you should know why we're doing what we're doing. I will explain that I've put the fastboot flash zip firmware.zip on here twice because, if you read the messages presented, it will tell you that hboot was applied and you need to send the zip over again right away.

Also, be patient with the system.img. If you've never flashed your system.img through this interface, it breaks the image up in pieces and sends it.. I think mine took 4 times.

adb reboot-bootloader
fastboot oem rebootRUU
fastboot flash system system.img
fastboot reboot-bootloader
fastboot oem rebootRUU
fastboot flash zip firmware.zip
fastboot flash zip firmware.zip
fastboot reboot-bootloader
fastboot flash recovery twrp-2.8.8.1-hiae.img

From the screen boot into recovery.

If you don't already have the SuperSU flashable zip on the phone, then you can either adb push it or go through the MTP device, but flash the SuperSU zip inside recovery and then reboot. The zip warns you not to let TWRP try to get root. I was not prompted by TWRP, but if you are DO NOT LET TWRP ROOT YOUR PHONE.

Once the phone started to boot, it went through the "Optimizing apps"... Then it did the handsfree activation. I can't remember if it asked me about security on THIS screen or the next time it booted, but it did apply the latest PRL and update the profile and then reboot again. Be patient through all this.

Some things to be aware of (your results may differ)... My wallpaper got wiped out through this process, but everything else remained. Sprint ID tried to run, but that could also be because I never let it run when I first got my phone (I disabled the app using Titanium), so I just disabled Sprint ID again and reset my wallpaper. Some system apps that I had disabled using Titanium were now enabled again. Facebook and Messenger that I had previously disabled got enabled again. So there I did spend another 10 minutes or so finding all those programs and disabling them again. Android Pay seems to be working for me. The fingerprint reader is still working for me.

I hope this helps someone who might be pulling their hair out trying to figure out how to update with the latest OTA.